The damage done to the ruins of ancient Babylon is visible from a small hilltop near the Tower of Babel, whose biblical importance is hard to envision from what is left of it today.

Across the horizon are guard towers, concertina wire and dirt-filled barriers among the palm trees; encroaching farms and concrete houses from this village and others; and the enormous palace that Saddam Hussein built in the 1980s atop the city where Nebuchadnezzar II ruled.

Something else is visible, too: earthen mounds concealing all that has yet to be discovered in a city that the prophet Jeremiah called “a gold cup in the Lord’s hands, a cup that made the whole earth drunk.”

On the hillside during one of his many visits to the ruins, Jeff Allen, a conservationist working with the World Monuments Fund, said: “All this is unexcavated. There is great potential at this site. You could excavate the street plan of the entire city.”

That is certainly years away given the realities of today’s Iraq. But for the first time since the American invasion in 2003, after years of neglect and violence, archaeologists and preservationists have once again begun working to protect and even restore parts of Babylon and other ancient ruins of Mesopotamia. And there are new sites being excavated for the first time, mostly in secret to avoid attracting the attention of looters, who remain a scourge here.

The World Monuments Fund, working with Iraq’s State Board of Antiquities and Heritage, has drafted a conservation plan to combat any further deterioration of Babylon’s mud-brick ruins and reverse some of the effects of time and Mr. Hussein’s propagandistic and archaeologically specious re-creations.

In November, the State Department announced a new $2 million grant to begin work to preserve the site’s most impressive surviving ruins. They include the foundation of the Ishtar Gate, built in the sixth century B.C. by Nebuchadnezzar’s father, Nabopolassar, and adorned with brick reliefs of the Babylonian gods Marduk and Adad. (The famous blue-glazed gate that Nebuchadnezzar commissioned was excavated in the early 20th century and rebuilt in the Pergamon Museum in Berlin.)

The objective is to prepare the site and other ruins — from Ur in the south to Nimrud in the north — for what officials hope will someday be a flood of scientists, scholars and tourists that could contribute to Iraq’s economic revival almost as much as oil.

The Babylon project is Iraq’s biggest and most ambitious by far, a reflection of the ancient city’s fame and its resonance in Iraq’s modern political and cultural heritage.

“This is one of the great projects we have, and it is the first,” Qais Hussein Rashid, the director of the State Board of Antiquities and Heritage, said in an interview in Baghdad. “We want to have it as a model for all the other sites.”

The task at hand is daunting, though, and the threats to the site abundant. In the case of some of the Hussein-era reconstructions, they are irreversible. The American invasion and the carnage that followed brought archaeological and preservation work to a halt across the country, leaving ruins to wither or, in the case of looting, much worse.

The American military turned Babylon into a base. It was later occupied by Polish troops and, though it was returned to the control of the State Board of Antiquities and Heritage in 2004, the detritus of a military presence still scars the site.

The World Monuments Fund has been carrying out what amounts to archaeological triage since it began its conservation plan in 2009. It has created computer scans to provide precise records of the damage to the ruins and identified the most pernicious threats, starting with erosion caused by salty groundwater. “What we’ve got to do is create a stable environment,” Mr. Allen said at the site in November. “Right now it’s on the fast road to falling apart.”

The wicking of groundwater into mud bricks, compounded by a modern concrete walkway and the excavations conducted by the German archaeologist Robert Koldewey more than a century ago, have already eaten away some of the 2,500-year-old brick reliefs at the Ishtar Gate’s base.

“They took care of Ishtar Gate only from the inside, because you had visiting leaders and dignitaries who would come,” said Mahmoud Bendakir, an architect who is working with the fund, referring to the site’s caretakers during the Hussein era. “The outside is a disaster.”

The grant from the United States will pay for repairs to channel the water away from the gate’s foundation, which stands several yards beneath the surrounding area. Similar repairs are planned for two of Babylon’s temples, Ninmakh and Nabu-sha-Khare, the most complete sets of ruins, though they too suffer from erosion and harmful restorations with modern bricks.

“It’s difficult to say which is doing more,” Mr. Allen said, “but the two together are nearly toxic for the preservation of monuments.”

The American reconstruction team has refurbished a modern museum on the site, as well as a model of the Ishtar Gate that for decades served as a visitors’ entrance. Inside the museum is one of the site’s most valuable relics: a glazed brick relief of a lion, one of 120 that once lined the processional way into the city.

The museum, with three galleries, is scheduled to open this month, receiving its first visitors since 2003. And with new security installed, talks are under way to return ancient Babylonian artifacts from the National Museum in Baghdad.

The fate of Babylon is already being disputed by Iraqi leaders, with antiquities officials clashing with local authorities over when to open it to visitors and how to exploit the site for tourism that, for the most part, remains a goal more than a reality. Even now they are clashing over whether the admission fee should go to the antiquities board or the provincial government.

Another of the more dire threats to the site has been unchecked development inside the boundaries of the old city walls, enclosing nearly three square miles. The fund’s project has plotted the old walls on a map, causing trepidation among Iraqis who live along them now.

They fear the preservation of Babylon’s ruins will force them from their homes and farmlands, as when Mr. Hussein expelled residents of a local village to build his palace. “They took them from their lands,” said Minshed al-Mamuri, who runs a civic organization for widows and orphans here. “It’s psychological for them.”

Mr. Allen, who oversees the fund’s work, said the preservation of Babylon would require collaboration among competing constituencies that is extremely rare amid Iraq’s political instability.

“We’re looking at not just archaeology,” he said of the project. “We’re looking at the economic opportunities and viability for local people. They need to see something out of this site. That’s possible, and possible at the same time to preserve the integrity of the site.”